GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ptsC in Shewanella amazonensis SB2B

Align IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized)
to candidate 6936959 Sama_1133 PTS system, glucose-specific IIBC component (RefSeq)

Query= TCDB::Q8GBT6
         (403 letters)



>lcl|FitnessBrowser__SB2B:6936959 Sama_1133 PTS system,
           glucose-specific IIBC component (RefSeq)
          Length = 485

 Score =  236 bits (601), Expect = 1e-66
 Identities = 137/391 (35%), Positives = 216/391 (55%), Gaps = 23/391 (5%)

Query: 5   QRIGRSLMLPVAVLPAAALLVRLGNADMLGRPEFPAFVTKIAG-FMAAGGNAILDNMALL 63
           QR+ ++L++P+A+LPAA +++ +    +        F+  +A   M + G  I D M +L
Sbjct: 24  QRLSQTLLIPIAILPAAGVMIGIATNPL-------PFIPDVANVLMLSVGKLIFDIMPML 76

Query: 64  FAVGIAIGFAKKSDGSTALAAVVGYLVFKNVLATFTDK-NLPQVAKAVDGKVVMVDAPVD 122
           FA+ +AIGF +   G  A +A  GY V  + LA      +LP         +V     +D
Sbjct: 77  FAIAVAIGFCR-DQGIAAFSAAFGYGVLLSTLAAAAKVYHLPS-------HIVWGTPTID 128

Query: 123 AKVLGGVVMGLVVALLYQRFYRTKLPDWAGFFGGRRLVPILSAFAGLVIGIVFGYIWPVL 182
             + GG+++G +  +  +   + +LP    FF GRR  P++     +++ ++  +IWP L
Sbjct: 129 TGIAGGMLVGGITCVAVRLSEKLRLPAVFSFFEGRRSAPLIMIPLVMLLAVMLAFIWPPL 188

Query: 183 GTGLHNFGEWLV-GSGAVGAGIFGVANRALIPIGMHHLLNSFPWFQAGEY----EGKSGD 237
              +    +W V    A+  G +G+  R L+P+G+HH+ N+  + + G+Y    E   G+
Sbjct: 189 ALSIERLSDWAVYQEPAIAFGFYGMVERLLLPLGLHHIWNAPFYLEVGQYAHDGEIVRGE 248

Query: 238 IARFLAGDPTAGQFMTGFFPIMMFALPAACLAIVHCARPERRKVVGGMMFSLALTSFVTG 297
           +AR+ AGDP+AG    G+  I M+ LPAA LAI  CA   +R  V G+M S A  S++TG
Sbjct: 249 MARYFAGDPSAGNLAGGYL-IKMWGLPAAALAIWRCADRNQRNRVAGVMLSAATASWLTG 307

Query: 298 VTEPIEFTFMFIAPVLYAIHAVLTGVSMALTWALGMKDGFGFSAGAVDFFLNLGIASNPW 357
           VTEPIEF F+F+AP+LY  HA+LTG++ ++   L M     FS G VDF L    +SN  
Sbjct: 308 VTEPIEFAFLFVAPLLYLCHALLTGLAYSIAILLDMHHSVVFSHGLVDFVLLFPQSSNTH 367

Query: 358 GLALVGVCFAALYYVVFRFAITKFNLPTPGR 388
            +  +G     +YY++FR +I  FNL TPGR
Sbjct: 368 WIWFLGPLTFVIYYILFRASILAFNLKTPGR 398


Lambda     K      H
   0.328    0.143    0.441 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 526
Number of extensions: 30
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 403
Length of database: 485
Length adjustment: 32
Effective length of query: 371
Effective length of database: 453
Effective search space:   168063
Effective search space used:   168063
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory